LAMMPS (27 Jun 2024)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
  using 1 OpenMP thread(s) per MPI task
# Solvated 5-mer peptide

units		real
atom_style	full

pair_style	lj/charmm/coul/long 8.0 10.0 10.0
bond_style      harmonic
angle_style     charmm
dihedral_style  charmm
improper_style  harmonic
kspace_style	pppm 0.0001

read_data	data.peptide
Reading data file ...
  orthogonal box = (36.840194 41.013691 29.768095) to (64.21156 68.385058 57.139462)
  1 by 2 by 2 MPI processor grid
  reading atoms ...
  2004 atoms
  reading velocities ...
  2004 velocities
  scanning bonds ...
  3 = max bonds/atom
  scanning angles ...
  6 = max angles/atom
  scanning dihedrals ...
  14 = max dihedrals/atom
  scanning impropers ...
  1 = max impropers/atom
  orthogonal box = (36.840194 41.013691 29.768095) to (64.21156 68.385058 57.139462)
  1 by 2 by 2 MPI processor grid
  reading bonds ...
  1365 bonds
  reading angles ...
  786 angles
  reading dihedrals ...
  207 dihedrals
  reading impropers ...
  12 impropers
Finding 1-2 1-3 1-4 neighbors ...
  special bond factors lj:    0        0        0       
  special bond factors coul:  0        0        0       
     4 = max # of 1-2 neighbors
     7 = max # of 1-3 neighbors
    14 = max # of 1-4 neighbors
    18 = max # of special neighbors
  special bonds CPU = 0.000 seconds
  read_data CPU = 0.011 seconds

neighbor	2.0 bin
neigh_modify	delay 5

timestep	2.0

group		peptide type <= 12
84 atoms in group peptide
group		one id 2 4 5 6
4 atoms in group one
group		two id 80 82 83 84
4 atoms in group two
group		ref id 37
1 atoms in group ref
group		colvar union one two ref
9 atoms in group colvar

fix		1 all nvt temp  275.0 275.0 100.0 tchain 1

shell "rm -f out*.colvars.*"
fix		2 all colvars peptide.colvars
----------------------------------------------------------------------
Initializing the collective variables module, version 2024-06-04.
Please cite Fiorin et al, Mol Phys 2013:
  https://doi.org/10.1080/00268976.2013.813594
as well as all other papers listed below for individual features used.
Please cite Fiorin et al, Mol Phys 2013:
  https://doi.org/10.1080/00268976.2013.813594
as well as all other papers listed below for individual features used.
Please cite Fiorin et al, Mol Phys 2013:
  https://doi.org/10.1080/00268976.2013.813594
as well as all other papers listed below for individual features used.
This version was built with the C++11 standard or higher.
Summary of compile-time features available in this build:
  - SMP parallelism: enabled (num. threads = 1)
  - Lepton custom functions: available
  - Tcl interpreter: not available
Using LAMMPS interface, version "2024-07-05".
fix		2a ref setforce 0.0 0.0 0.0

fix		4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
Finding SHAKE clusters ...
      19 = # of size 2 clusters
       6 = # of size 3 clusters
       3 = # of size 4 clusters
     640 = # of frozen angles
  find clusters CPU = 0.000 seconds

#dump		1 colvar custom 1 dump.colvar.lammpstrj id xu yu zu fx fy fz
#dump_modify 1 sort id

thermo_style	custom step temp etotal pe ke epair ebond f_2
thermo		10


run		100

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Your simulation uses code contributions which should be cited:

- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419

@Article{Gissinger24,
 author = {Jacob R. Gissinger, Ilia Nikiforov, Yaser Afshar, Brendon Waters, Moon-ki Choi, Daniel S. Karls, Alexander Stukowski, Wonpil Im, Hendrik Heinz, Axel Kohlmeyer, and Ellad B. Tadmor},
 title = {Type Label Framework for Bonded Force Fields in LAMMPS},
 journal = {J. Phys. Chem. B},
 year =    2024,
 volume =  128,
 number =  13,
 pages =   {3282–-3297}
}

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

PPPM initialization ...
  using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
  G vector (1/distance) = 0.26872465
  grid = 15 15 15
  stencil order = 5
  estimated absolute RMS force accuracy = 0.022820853
  estimated relative force accuracy = 6.872432e-05
  using double precision FFTW3
  3d grid and FFT values/proc = 4312 960
Generated 91 of 91 mixed pair_coeff terms from arithmetic mixing rule
Neighbor list info ...
  update: every = 1 steps, delay = 5 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 12
  ghost atom cutoff = 12
  binsize = 6, bins = 5 5 5
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair lj/charmm/coul/long, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/3d
      bin: standard
----------------------------------------------------------------------
Reading new configuration from file "peptide.colvars":
# units = "" [default]
# smp = on [default]
# colvarsTrajFrequency = 1
# colvarsRestartFrequency = 1000
# scriptedColvarForces = off [default]
# scriptingAfterBiases = off [default]
----------------------------------------------------------------------
  Initializing a new collective variable.
  # name = "one"
  Initializing a new "distance" component.
    # name = "" [default]
    # componentCoeff = 1 [default]
    # componentExp = 1 [default]
    # period = 0 [default]
    # wrapAround = 0 [default]
    # forceNoPBC = off [default]
    # scalable = on [default]
      Initializing atom group "group1".
      # name = "" [default]
      # centerToOrigin = off [default]
      # centerToReference = off [default]
      # rotateToReference = off [default]
      # atomsOfGroup = "" [default]
      # indexGroup = "" [default]
      # psfSegID =  [default]
      # atomsFile = "" [default]
      # dummyAtom = ( 0 , 0 , 0 ) [default]
      # enableFitGradients = on [default]
      # printAtomIDs = off [default]
      Atom group "group1" defined with 4 atoms requested.
      Initializing atom group "group2".
      # name = "" [default]
      # centerToOrigin = off [default]
      # centerToReference = off [default]
      # rotateToReference = off [default]
      # atomsOfGroup = "" [default]
      # indexGroup = "" [default]
      # psfSegID =  [default]
      # atomsFile = "" [default]
      # dummyAtom = ( 0 , 0 , 0 ) [default]
      # enableFitGradients = on [default]
      # printAtomIDs = off [default]
      Atom group "group2" defined with 1 atoms requested.
    # oneSiteSystemForce = off [default]
    # oneSiteTotalForce = off [default]
  All components initialized.
  # timeStepFactor = 1 [default]
  # width = 1 [default]
  # lowerBoundary = 0 [default]
  # upperBoundary = 1 [default]
  # hardLowerBoundary = on [default]
  # hardUpperBoundary = off [default]
  # expandBoundaries = off [default]
  # extendedLagrangian = off [default]
  # outputValue = on [default]
  # outputVelocity = off [default]
  # outputTotalForce = off [default]
  # outputAppliedForce = off [default]
  # subtractAppliedForce = off [default]
  # runAve = off [default]
  # corrFunc = off [default]
----------------------------------------------------------------------
  Initializing a new collective variable.
  # name = "two"
  Initializing a new "distance" component.
    # name = "" [default]
    # componentCoeff = 1 [default]
    # componentExp = 1 [default]
    # period = 0 [default]
    # wrapAround = 0 [default]
    # forceNoPBC = off [default]
    # scalable = on [default]
      Initializing atom group "group1".
      # name = "" [default]
      # centerToOrigin = off [default]
      # centerToReference = off [default]
      # rotateToReference = off [default]
      # atomsOfGroup = "" [default]
      # indexGroup = "" [default]
      # psfSegID =  [default]
      # atomsFile = "" [default]
      # dummyAtom = ( 0 , 0 , 0 ) [default]
      # enableFitGradients = on [default]
      # printAtomIDs = off [default]
      Atom group "group1" defined with 4 atoms requested.
      Initializing atom group "group2".
      # name = "" [default]
      # centerToOrigin = off [default]
      # centerToReference = off [default]
      # rotateToReference = off [default]
      # atomsOfGroup = "" [default]
      # indexGroup = "" [default]
      # psfSegID =  [default]
      # atomsFile = "" [default]
      # dummyAtom = ( 0 , 0 , 0 ) [default]
      # enableFitGradients = on [default]
      # printAtomIDs = off [default]
      Atom group "group2" defined with 1 atoms requested.
    # oneSiteSystemForce = off [default]
    # oneSiteTotalForce = off [default]
  All components initialized.
  # timeStepFactor = 1 [default]
  # width = 1 [default]
  # lowerBoundary = 0 [default]
  # upperBoundary = 1 [default]
  # hardLowerBoundary = on [default]
  # hardUpperBoundary = off [default]
  # expandBoundaries = off [default]
  # extendedLagrangian = off [default]
  # outputValue = on [default]
  # outputVelocity = off [default]
  # outputTotalForce = off [default]
  # outputAppliedForce = off [default]
  # subtractAppliedForce = off [default]
  # runAve = off [default]
  # corrFunc = off [default]
----------------------------------------------------------------------
Collective variables initialized, 2 in total.
----------------------------------------------------------------------
  Initializing a new "harmonic" instance.
  # name = "h_pot"
  # colvars = { one, two }
  # stepZeroData = off [default]
  # outputEnergy = off [default]
  # outputFreq = 1000 [default]
  # timeStepFactor = 1 [default]
  # writeTISamples = off [default]
  # writeTIPMF = off [default]
  # centers = { 10, 10 }
  # targetCenters = { 10, 10 } [default]
  # outputCenters = off [default]
  # forceConstant = 100
  # decoupling = off [default]
  # targetForceConstant = -1 [default]
  The force constant for colvar "one" will be rescaled to 100 according to the specified width (1).
  The force constant for colvar "two" will be rescaled to 100 according to the specified width (1).
----------------------------------------------------------------------
Collective variables biases initialized, 1 in total.
----------------------------------------------------------------------
Collective variables module (re)initialized.
----------------------------------------------------------------------
Current simulation parameters: initial step = 0, integration timestep = 2
Updating atomic parameters (masses, charges, etc).
Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 15.035, total charge = -2.77556e-17.
Re-initialized atom group for variable "one":0/1. 1 atoms: total mass = 12.011, total charge = 0.51.
Re-initialized atom group for variable "two":0/0. 4 atoms: total mass = 15.035, total charge = 0.16.
Re-initialized atom group for variable "two":0/1. 1 atoms: total mass = 12.011, total charge = 0.51.
The final output state file will be "out.colvars.state".
Synchronizing (emptying the buffer of) trajectory file "out.colvars.traj".
SHAKE stats (type/ave/delta/count) on step 0
Bond:    4   1.111     1.44264e-05        9
Bond:    6   0.996998  7.26967e-06        6
Bond:    8   1.08      1.32536e-05        7
Bond:   10   1.111     1.22749e-05        8
Bond:   12   1.08      1.11767e-05        9
Bond:   14   0.96      0                  1
Bond:   18   0.957206  4.37979e-05     1280
Angle:  31   104.519   0.00396029       640
Per MPI rank memory allocation (min/avg/max) = 16.02 | 16.22 | 16.41 Mbytes
   Step          Temp          TotEng         PotEng         KinEng         E_pair         E_bond          f_2      
         0   282.10052     -5237.458      -6372.3766      1134.9186     -6442.768       16.557152      292.14604    
        10   305.06149     -5058.8972     -6286.1901      1227.2929     -6413.1021      58.8499        103.38345    
        20   311.00516     -4999.0612     -6250.266       1251.2048     -6417.1021      47.695297      36.699695    
        30   314.22337     -4993.7012     -6257.8532      1264.152      -6421.9679      35.344144      10.563933    
        40   297.87491     -5020.8378     -6219.2184      1198.3805     -6389.8528      27.723133      3.8354517    
        50   304.02071     -5056.2576     -6279.3633      1223.1057     -6456.8214      55.459505      0.20678217   
        60   285.92576     -5104.0461     -6254.354       1150.3079     -6435.5814      32.767229      0.69352945   
        70   277.83519     -5163.9758     -6281.7345      1117.7587     -6447.7033      39.627168      11.433603    
        80   267.51495     -5206.4046     -6282.644       1076.2394     -6456.6369      31.611883      6.3554178    
        90   278.15579     -5245.3824     -6364.431       1119.0485     -6499.8063      28.849773      0.36941576   
SHAKE stats (type/ave/delta/count) on step 100
Bond:    4   1.11098   8.97155e-05        9
Bond:    6   0.996996  1.00568e-05        6
Bond:    8   1.08      6.02345e-06        7
Bond:   10   1.111     1.84253e-05        8
Bond:   12   1.08      7.2713e-06         9
Bond:   14   0.959996  0                  1
Bond:   18   0.957198  3.36079e-05     1280
Angle:  31   104.52    0.0030599        640
       100   260.10613     -5292.6885     -6339.1215      1046.433      -6471.6734      25.362042      0.21987323   
Saving collective variables state to "out.colvars.state".
Loop time of 0.246405 on 4 procs for 100 steps with 2004 atoms

Performance: 70.128 ns/day, 0.342 hours/ns, 405.836 timesteps/s, 813.295 katom-step/s
99.5% CPU use with 4 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.17765    | 0.18092    | 0.18373    |   0.6 | 73.42
Bond    | 0.00021581 | 0.00045219 | 0.00069916 |   0.0 |  0.18
Kspace  | 0.018035   | 0.020459   | 0.023812   |   1.7 |  8.30
Neigh   | 0.032165   | 0.032193   | 0.032207   |   0.0 | 13.07
Comm    | 0.00566    | 0.0058533  | 0.0060088  |   0.2 |  2.38
Output  | 0.00012205 | 0.00014069 | 0.00019404 |   0.0 |  0.06
Modify  | 0.0059979  | 0.0060225  | 0.0060368  |   0.0 |  2.44
Other   |            | 0.0003631  |            |       |  0.15

Nlocal:            501 ave         513 max         489 min
Histogram: 1 0 0 0 1 1 0 0 0 1
Nghost:        6563.25 ave        6596 max        6519 min
Histogram: 1 0 1 0 0 0 0 0 0 2
Neighs:         177059 ave      181742 max      172942 min
Histogram: 1 0 1 0 0 0 1 0 0 1

Total # of neighbors = 708237
Ave neighs/atom = 353.41168
Ave special neighs/atom = 2.3403194
Neighbor list builds = 12
Dangerous builds = 2

run     100

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Your simulation uses code contributions which should be cited:

- Colvars module (Fiorin2013, plus other works listed for specific features)


% Colvars module:
% Colvars-LAMMPS interface:
% Harmonic colvar bias implementation:
% Optimal rotation via flexible fitting:
% distance colvar component:

@article{Fiorin2013,
  author = {Fiorin, Giacomo and Klein, Michael L.{} and H\'enin, J\'er\^ome},
  title = {Using collective variables to drive molecular dynamics simulations},
  journal = {Mol. Phys.},
  year = {2013},
  volume = {111},
  number = {22-23},
  pages = {3345--3362},
  publisher = {Taylor & Francis},
  doi = {10.1080/00268976.2013.813594},
  url = {https://doi.org/10.1080/00268976.2013.813594}
}


% LAMMPS engine:

@article{Thompson2022,
  title = {{LAMMPS} - a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales},
  author = {Thompson, Aidan P. and Aktulga, H. Metin and Berger, Richard and Bolintineanu, Dan S. and Brown, W. Michael and Crozier, Paul S. and {in't Veld}, Pieter J. and Kohlmeyer, Axel and Moore, Stan G. and Nguyen, Trung Dac and Shan, Ray and Stevens, Mark J. and Tranchida, Julien and Trott, Christian and Plimpton, Steven J.},
  journal = {Comp. Phys. Comm.},
  volume = {271},
  pages = {108171},
  year = {2022},
  doi = {10.1016/j.cpc.2021.108171},
  url = {https://doi.org/10.1016/j.cpc.2021.108171}
}

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

PPPM initialization ...
  using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
  G vector (1/distance) = 0.26872465
  grid = 15 15 15
  stencil order = 5
  estimated absolute RMS force accuracy = 0.022820853
  estimated relative force accuracy = 6.872432e-05
  using double precision FFTW3
  3d grid and FFT values/proc = 4312 960
Generated 91 of 91 mixed pair_coeff terms from arithmetic mixing rule
Current simulation parameters: initial step = 100, integration timestep = 2
Updating atomic parameters (masses, charges, etc).
Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 15.035, total charge = -2.77556e-17.
Re-initialized atom group for variable "one":0/1. 1 atoms: total mass = 12.011, total charge = 0.51.
Re-initialized atom group for variable "two":0/0. 4 atoms: total mass = 15.035, total charge = 0.16.
Re-initialized atom group for variable "two":0/1. 1 atoms: total mass = 12.011, total charge = 0.51.
SHAKE stats (type/ave/delta/count) on step 100
Bond:    4   1.11098   8.97155e-05        9
Bond:    6   0.996996  1.00568e-05        6
Bond:    8   1.08      6.02345e-06        7
Bond:   10   1.111     1.84253e-05        8
Bond:   12   1.08      7.2713e-06         9
Bond:   14   0.959996  0                  1
Bond:   18   0.957198  3.36079e-05     1280
Angle:  31   104.52    0.0030599        640
Per MPI rank memory allocation (min/avg/max) = 16.02 | 16.22 | 16.41 Mbytes
   Step          Temp          TotEng         PotEng         KinEng         E_pair         E_bond          f_2      
       100   260.10613     -5292.6885     -6339.1215      1046.433      -6471.6734      25.362042      0.21987323   
       110   266.26438     -5341.1991     -6412.4073      1071.2082     -6552.7551      33.573173      1.9229657    
       120   262.66604     -5386.2387     -6442.9704      1056.7317     -6587.5483      29.859587      2.7124812    
       130   252.83379     -5422.5401     -6439.7157      1017.1756     -6580.4703      25.979343      1.2031591    
       140   253.85111     -5452.1837     -6473.4521      1021.2684     -6609.4826      26.071651      0.30585517   
       150   261.31816     -5490.4726     -6541.7816      1051.3091     -6646.6075      16.258823      6.9051008    
       160   255.7352      -5521.5941     -6550.4423      1028.8483     -6658.1373      19.717399      12.339679    
       170   253.42527     -5540.0942     -6559.6494      1019.5552     -6656.6678      23.293812      10.290217    
       180   248.51161     -5550.3254     -6550.1125      999.78704     -6661.4235      26.200127      3.4336036    
       190   250.80862     -5555.2555     -6564.2836      1009.0281     -6666.164       25.53634       3.3494286    
SHAKE stats (type/ave/delta/count) on step 200
Bond:    4   1.111     1.81266e-06        9
Bond:    6   0.997     7.79424e-07        6
Bond:    8   1.08      1.08903e-06        7
Bond:   10   1.111     2.96503e-07        8
Bond:   12   1.08      4.69038e-07        9
Bond:   14   0.960001  0                  1
Bond:   18   0.957201  3.76471e-06     1280
Angle:  31   104.52    0.000411055      640
       200   251.50475     -5557.4252     -6569.2539      1011.8288     -6674.0846      24.804906      7.1387572    
Saving collective variables state to "out.colvars.state".
Loop time of 0.238087 on 4 procs for 100 steps with 2004 atoms

Performance: 72.578 ns/day, 0.331 hours/ns, 420.014 timesteps/s, 841.709 katom-step/s
99.4% CPU use with 4 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.17913    | 0.18408    | 0.19082    |   1.1 | 77.32
Bond    | 0.00019617 | 0.00044139 | 0.00071286 |   0.0 |  0.19
Kspace  | 0.016186   | 0.022449   | 0.02737    |   3.0 |  9.43
Neigh   | 0.018728   | 0.018753   | 0.018777   |   0.0 |  7.88
Comm    | 0.0052171  | 0.0055397  | 0.0058422  |   0.3 |  2.33
Output  | 0.00012326 | 0.00014453 | 0.00020506 |   0.0 |  0.06
Modify  | 0.0062505  | 0.0062725  | 0.0062944  |   0.0 |  2.63
Other   |            | 0.0004069  |            |       |  0.17

Nlocal:            501 ave         513 max         481 min
Histogram: 1 0 0 0 0 0 1 0 1 1
Nghost:         6556.5 ave        6608 max        6514 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Neighs:         177021 ave      182259 max      172089 min
Histogram: 2 0 0 0 0 0 0 0 1 1

Total # of neighbors = 708083
Ave neighs/atom = 353.33483
Ave special neighs/atom = 2.3403194
Neighbor list builds = 7
Dangerous builds = 0

fix 2 all colvars peptide.colvars input out.colvars.state output out2
----------------------------------------------------------------------
Initializing the collective variables module, version 2024-06-04.
Please cite Fiorin et al, Mol Phys 2013:
  https://doi.org/10.1080/00268976.2013.813594
as well as all other papers listed below for individual features used.
Please cite Fiorin et al, Mol Phys 2013:
  https://doi.org/10.1080/00268976.2013.813594
as well as all other papers listed below for individual features used.
Please cite Fiorin et al, Mol Phys 2013:
  https://doi.org/10.1080/00268976.2013.813594
as well as all other papers listed below for individual features used.
This version was built with the C++11 standard or higher.
Summary of compile-time features available in this build:
  - SMP parallelism: enabled (num. threads = 1)
  - Lepton custom functions: available
  - Tcl interpreter: not available
Using LAMMPS interface, version "2024-07-05".
Setting initial step number from MD engine: 200

run     100
PPPM initialization ...
  using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
  G vector (1/distance) = 0.26872465
  grid = 15 15 15
  stencil order = 5
  estimated absolute RMS force accuracy = 0.022820853
  estimated relative force accuracy = 6.872432e-05
  using double precision FFTW3
  3d grid and FFT values/proc = 4312 960
Generated 91 of 91 mixed pair_coeff terms from arithmetic mixing rule
Will read input state from file "out.colvars.state"----------------------------------------------------------------------
Reading new configuration from file "peptide.colvars":
# units = "" [default]
# smp = on [default]
# colvarsTrajFrequency = 1
# colvarsRestartFrequency = 1000
# scriptedColvarForces = off [default]
# scriptingAfterBiases = off [default]
----------------------------------------------------------------------
  Initializing a new collective variable.
  # name = "one"
  Initializing a new "distance" component.
    # name = "" [default]
    # componentCoeff = 1 [default]
    # componentExp = 1 [default]
    # period = 0 [default]
    # wrapAround = 0 [default]
    # forceNoPBC = off [default]
    # scalable = on [default]
      Initializing atom group "group1".
      # name = "" [default]
      # centerToOrigin = off [default]
      # centerToReference = off [default]
      # rotateToReference = off [default]
      # atomsOfGroup = "" [default]
      # indexGroup = "" [default]
      # psfSegID =  [default]
      # atomsFile = "" [default]
      # dummyAtom = ( 0 , 0 , 0 ) [default]
      # enableFitGradients = on [default]
      # printAtomIDs = off [default]
      Atom group "group1" defined with 4 atoms requested.
      Initializing atom group "group2".
      # name = "" [default]
      # centerToOrigin = off [default]
      # centerToReference = off [default]
      # rotateToReference = off [default]
      # atomsOfGroup = "" [default]
      # indexGroup = "" [default]
      # psfSegID =  [default]
      # atomsFile = "" [default]
      # dummyAtom = ( 0 , 0 , 0 ) [default]
      # enableFitGradients = on [default]
      # printAtomIDs = off [default]
      Atom group "group2" defined with 1 atoms requested.
    # oneSiteSystemForce = off [default]
    # oneSiteTotalForce = off [default]
  All components initialized.
  # timeStepFactor = 1 [default]
  # width = 1 [default]
  # lowerBoundary = 0 [default]
  # upperBoundary = 1 [default]
  # hardLowerBoundary = on [default]
  # hardUpperBoundary = off [default]
  # expandBoundaries = off [default]
  # extendedLagrangian = off [default]
  # outputValue = on [default]
  # outputVelocity = off [default]
  # outputTotalForce = off [default]
  # outputAppliedForce = off [default]
  # subtractAppliedForce = off [default]
  # runAve = off [default]
  # corrFunc = off [default]
----------------------------------------------------------------------
  Initializing a new collective variable.
  # name = "two"
  Initializing a new "distance" component.
    # name = "" [default]
    # componentCoeff = 1 [default]
    # componentExp = 1 [default]
    # period = 0 [default]
    # wrapAround = 0 [default]
    # forceNoPBC = off [default]
    # scalable = on [default]
      Initializing atom group "group1".
      # name = "" [default]
      # centerToOrigin = off [default]
      # centerToReference = off [default]
      # rotateToReference = off [default]
      # atomsOfGroup = "" [default]
      # indexGroup = "" [default]
      # psfSegID =  [default]
      # atomsFile = "" [default]
      # dummyAtom = ( 0 , 0 , 0 ) [default]
      # enableFitGradients = on [default]
      # printAtomIDs = off [default]
      Atom group "group1" defined with 4 atoms requested.
      Initializing atom group "group2".
      # name = "" [default]
      # centerToOrigin = off [default]
      # centerToReference = off [default]
      # rotateToReference = off [default]
      # atomsOfGroup = "" [default]
      # indexGroup = "" [default]
      # psfSegID =  [default]
      # atomsFile = "" [default]
      # dummyAtom = ( 0 , 0 , 0 ) [default]
      # enableFitGradients = on [default]
      # printAtomIDs = off [default]
      Atom group "group2" defined with 1 atoms requested.
    # oneSiteSystemForce = off [default]
    # oneSiteTotalForce = off [default]
  All components initialized.
  # timeStepFactor = 1 [default]
  # width = 1 [default]
  # lowerBoundary = 0 [default]
  # upperBoundary = 1 [default]
  # hardLowerBoundary = on [default]
  # hardUpperBoundary = off [default]
  # expandBoundaries = off [default]
  # extendedLagrangian = off [default]
  # outputValue = on [default]
  # outputVelocity = off [default]
  # outputTotalForce = off [default]
  # outputAppliedForce = off [default]
  # subtractAppliedForce = off [default]
  # runAve = off [default]
  # corrFunc = off [default]
----------------------------------------------------------------------
Collective variables initialized, 2 in total.
----------------------------------------------------------------------
  Initializing a new "harmonic" instance.
  # name = "h_pot"
  # colvars = { one, two }
  # stepZeroData = off [default]
  # outputEnergy = off [default]
  # outputFreq = 1000 [default]
  # timeStepFactor = 1 [default]
  # writeTISamples = off [default]
  # writeTIPMF = off [default]
  # centers = { 10, 10 }
  # targetCenters = { 10, 10 } [default]
  # outputCenters = off [default]
  # forceConstant = 100
  # decoupling = off [default]
  # targetForceConstant = -1 [default]
  The force constant for colvar "one" will be rescaled to 100 according to the specified width (1).
  The force constant for colvar "two" will be rescaled to 100 according to the specified width (1).
----------------------------------------------------------------------
Collective variables biases initialized, 1 in total.
----------------------------------------------------------------------
Collective variables module (re)initialized.
----------------------------------------------------------------------
Current simulation parameters: initial step = 200, integration timestep = 2
Updating atomic parameters (masses, charges, etc).
Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 15.035, total charge = -2.77556e-17.
Re-initialized atom group for variable "one":0/1. 1 atoms: total mass = 12.011, total charge = 0.51.
Re-initialized atom group for variable "two":0/0. 4 atoms: total mass = 15.035, total charge = 0.16.
Re-initialized atom group for variable "two":0/1. 1 atoms: total mass = 12.011, total charge = 0.51.
----------------------------------------------------------------------
Loading state from text file "out.colvars.state".
  Restarting collective variable "one" from value: 10.0128
  Restarting collective variable "two" from value: 9.62236
  Restarted harmonic bias "h_pot" with step number 200.
----------------------------------------------------------------------
The final output state file will be "out2.colvars.state".
SHAKE stats (type/ave/delta/count) on step 200
Bond:    4   1.111     1.81266e-06        9
Bond:    6   0.997     7.79424e-07        6
Bond:    8   1.08      1.08903e-06        7
Bond:   10   1.111     2.96503e-07        8
Bond:   12   1.08      4.69038e-07        9
Bond:   14   0.960001  0                  1
Bond:   18   0.957201  3.76471e-06     1280
Angle:  31   104.52    0.000411055      640
Per MPI rank memory allocation (min/avg/max) = 16.02 | 16.22 | 16.41 Mbytes
   Step          Temp          TotEng         PotEng         KinEng         E_pair         E_bond          f_2      
       200   251.50475     -5557.4252     -6569.2539      1011.8288     -6674.0846      24.804906      7.1387572    
       210   253.15302     -5538.5615     -6557.0215      1018.4599     -6672.0498      37.676621      0.61219488   
       220   245.19621     -5522.5191     -6508.9679      986.44887     -6628.1899      36.657688      0.048643387  
       230   258.69885     -5495.7275     -6536.4989      1040.7713     -6658.2886      34.857911      0.22092559   
       240   260.79633     -5469.8678     -6519.0775      1049.2097     -6624.18        31.576952      3.7574815    
       250   269.07527     -5438.3946     -6520.9113      1082.5167     -6616.4382      25.447675      8.6600023    
       260   266.01046     -5397.3485     -6467.5352      1070.1867     -6580.2896      26.871919      8.3323104    
       270   272.81307     -5350.8819     -6448.4362      1097.5543     -6563.8228      23.114196      10.973132    
       280   279.42265     -5307.9799     -6432.1251      1124.1452     -6557.3368      33.644022      8.5490489    
       290   286.85168     -5260.841      -6414.874       1154.033      -6515.6797      28.574838      5.9100102    
SHAKE stats (type/ave/delta/count) on step 300
Bond:    4   1.111     1.79793e-05        9
Bond:    6   0.997005  1.02512e-05        6
Bond:    8   1.08      1.85103e-05        7
Bond:   10   1.111     9.9884e-06         8
Bond:   12   1.08      8.84114e-06        9
Bond:   14   0.960008  0                  1
Bond:   18   0.957203  1.8445e-05      1280
Angle:  31   104.52    0.00168383       640
       300   291.52793     -5216.288      -6389.1341      1172.846      -6503.1275      27.88915       2.2482428    
Saving collective variables state to "out2.colvars.state".
Loop time of 0.245933 on 4 procs for 100 steps with 2004 atoms

Performance: 70.263 ns/day, 0.342 hours/ns, 406.614 timesteps/s, 814.854 katom-step/s
99.6% CPU use with 4 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.17862    | 0.18666    | 0.19126    |   1.2 | 75.90
Bond    | 0.00021974 | 0.00048505 | 0.00077708 |   0.0 |  0.20
Kspace  | 0.018338   | 0.02317    | 0.031148   |   3.4 |  9.42
Neigh   | 0.022128   | 0.022183   | 0.022222   |   0.0 |  9.02
Comm    | 0.0059137  | 0.0060593  | 0.0064247  |   0.3 |  2.46
Output  | 0.00014648 | 0.00015946 | 0.00019596 |   0.0 |  0.06
Modify  | 0.0067012  | 0.00674    | 0.0067814  |   0.0 |  2.74
Other   |            | 0.0004738  |            |       |  0.19

Nlocal:            501 ave         513 max         472 min
Histogram: 1 0 0 0 0 0 0 0 0 3
Nghost:        6612.75 ave        6681 max        6561 min
Histogram: 1 1 0 0 0 1 0 0 0 1
Neighs:         177038 ave      180136 max      170218 min
Histogram: 1 0 0 0 0 0 0 1 0 2

Total # of neighbors = 708152
Ave neighs/atom = 353.36926
Ave special neighs/atom = 2.3403194
Neighbor list builds = 8
Dangerous builds = 0

Total wall time: 0:00:00
